Papers › SAM & SAM 2 in 3D Slicer: SegmentWithSAM Extension for Annotating Medical Images
SAM & SAM 2 in 3D Slicer: SegmentWithSAM Extension for Annotating Medical Images
Zafer Yildiz, YuWen Chen, Maciej A. Mazurowski
Creating annotations for 3D medical data is time-consuming and often requires highly specialized expertise. Various tools have been implemented to aid this process. Segment Anything Model 2 (SAM 2) offers a general-purpose prompt-based segmentation algorithm designed to annotate videos. In this paper, we adapt this model to the annotation of 3D medical images and offer our implementation in the form of an extension to the popular annotation software: 3D Slicer. Our extension allows users to place point prompts on 2D slices to generate annotation masks and propagate these annotations across entire volumes in either single-directional or bi-directional manners. Our code is publicly available on https://github.com/mazurowski-lab/SlicerSegmentWithSAM and can be easily installed directly from the Extension Manager of 3D Slicer as well.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections